Draft Genome Sequences of Mycobacterium tuberculosis Clinical Isolates from the Ural Region of Russia That Carry the pks15/1 Gene.

Here, we report the draft genome sequences of 15 Mycobacterium tuberculosis isolates of the Beijing-B0/W-148 sublineage that carry a 7-bp insertion within the pks15 gene, which leads to the synthesis of Pks15/1 fusion protein. Pks15/1 is involved in phenolglycolipid synthesis and biofilm formation, thus potentially contributing to the B0/W-148 lineage's enhanced virulence and drug resistance.

ANNOUNCEMENT

Mycobacterium tuberculosis virulence and pathogenicity are determined by a set of genes which are polymorphic in different phylogenetic lineages (1–3). The M. tuberculosis Beijing genotype has the widest spread; in Russia, it includes the “successful” clone Beijing B0/W-148, which is characterized as multidrug resistant (MDR) and highly virulent (4–6). Therefore, it is very important to analyze lineage-specific virulence and pathogenicity markers. One significant marker is the 7-bp insertion in the pks15 gene (CCGCGGC) that leads to the synthesis of an active fused Pks15/1 protein (7). Presence of the pks15/1 gene is correlated with highly virulent and drug-resistant strains of the Beijing genotype (8–10); it plays a significant role in virulence (via phenolic glycolipid synthesis) and may be involved in drug tolerance mediated by biofilm formation (7, 9, 11). Studying the genetic variability of virulence factors such as pks15/1 is essential for understanding the M. tuberculosis evolutionary process, including the evolution of host-pathogen interaction mechanisms and drug resistance. Thus, we provide the whole-genome sequencing data of 15 strains from a collection of 100 MDR M. tuberculosis Beijing-B0/W-148 strains (12) that carry a copy of the fused pks15/1 gene.

M. tuberculosis was cultured in Middlebrook 7H9 medium with the addition of oleic acid-albumin-dextrose-catalase (OADC; HiMedia, India) at 37°C for 4 weeks. Genomic DNA was isolated and purified by phenol-chloroform/isoamyl alcohol extraction after enzymatic cell lysis, as described by Belisle et al. (13). The quality of DNA was checked using gel electrophoresis and a Bioanalyzer 2100 instrument (Agilent Technologies, USA). Genomic DNA libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, USA). The raw sequencing data were obtained using the HiSeq 2500 platform (Illumina, USA) in rapid run mode with a HiSeq Rapid sequencing by synthesis (SBS) kit v2 (2 ×100 bp; Illumina). The quality check of the reads was done using FastQC v.0.11.7 (14). Illumina reads were de novo assembled using SPAdes v.3.12.0 (15) with the -careful flag and k-mers of 21, 33, 55, and 77, while assembly metrics were calculated with QUAST v.5.0.2 with default parameters (16). Automatic functional annotation results were obtained using the NCBI Prokaryotic Genome Annotation Pipeline. Characteristics of the sequenced genomes are listed in Table 1.

TABLE 1

Characteristics of 15 M. tuberculosis genome assemblies with the pks15/1 gene

Isolate	WGS (GenBank) accession no.	SRA accession no.	Genome size (bp)	GC content (%)	Coverage (×)	No. of contigs	Total no. of CDSsa
EKB1	VOVK00000000	SRR8327216	4,366,764	65.2	99	120	139
EKB3	VOVL00000000	SRR8327860	4,366,227	64.5	99	129	141
EKB10	VOVM00000000	SRR8442761	4,372,733	65.5	100	143	139
EKB12	VOVN00000000	SRR8335026	4,366,328	65.6	99	113	139
EKB23	VOVO00000000	SRR8347538	4,365,633	65.5	99	105	141
EKB28	VOVP00000000	SRR8351921	4,362,713	65.5	99	95	138
EKB29	VOVQ00000000	SRR8352462	4,366,364	65.1	100	129	143
EKB35	VOVR00000000	SRR8353483	4,365,172	65.4	99	106	143
EKB37	VOVS00000000	SRR8354336	4,364,827	65.4	99	108	136
EKB40	VOVT00000000	SRR8354717	4,359,315	65.4	99	103	145
EKB46	VOVU00000000	SRR8357446	4,358,597	65.4	99	100	135
EKB59	VOVV00000000	SRR8365894	4,367,947	65.3	99	121	134
EKB75	VOVW00000000	SRR8369894	4,361,209	64.3	99	121	143
EKB77	VOVX00000000	SRR8370130	4,361,099	65.0	99	123	144
EKB84	VOVY00000000	SRR8379901	4,360,816	65.0	99	132	144

CDS, coding sequence.

Data availability.

The whole-genome shotgun (WGS) assemblies described here have been deposited in NCBI GenBank. The versions described in this paper are the first versions. The read archives have been deposited in NCBI SRA. The WGS (GenBank) and SRA accession numbers are listed in Table 1. All of the data are part of BioProject identifier (ID) PRJNA509547.